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Detailed information for vg1020720683:

Variant ID: vg1020720683 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 20720683
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, C: 0.03, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


AATAGAGACACAGAGACTGAATTGAGCATCCCTTTTCAAACAAGAGTTTACATGGGAATTTATATTTCATTTTATCATCCCGGGGCAGCTCTAGGGTGAG[C/T]
TCCTCGATCCCAGGGATAGCTGCATCAAGCCAATGGTTGATATGATGGGCAGACAACTCATGAAAAAATTGTAGTTCAAACCTAAACCTCTTCACCCAAC

Reverse complement sequence

GTTGGGTGAAGAGGTTTAGGTTTGAACTACAATTTTTTCATGAGTTGTCTGCCCATCATATCAACCATTGGCTTGATGCAGCTATCCCTGGGATCGAGGA[G/A]
CTCACCCTAGAGCTGCCCCGGGATGATAAAATGAAATATAAATTCCCATGTAAACTCTTGTTTGAAAAGGGATGCTCAATTCAGTCTCTGTGTCTCTATT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 35.70% 4.10% 0.55% 59.63% NA
All Indica  2759 2.20% 1.00% 0.58% 96.23% NA
All Japonica  1512 96.00% 0.70% 0.20% 3.11% NA
Aus  269 43.90% 27.50% 0.74% 27.88% NA
Indica I  595 2.90% 0.80% 0.84% 95.46% NA
Indica II  465 1.30% 0.40% 0.43% 97.85% NA
Indica III  913 1.00% 0.20% 0.33% 98.47% NA
Indica Intermediate  786 3.60% 2.40% 0.76% 93.26% NA
Temperate Japonica  767 98.30% 0.00% 0.00% 1.69% NA
Tropical Japonica  504 93.50% 0.80% 0.40% 5.36% NA
Japonica Intermediate  241 94.20% 2.50% 0.41% 2.90% NA
VI/Aromatic  96 19.80% 75.00% 1.04% 4.17% NA
Intermediate  90 42.20% 12.20% 4.44% 41.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1020720683 C -> T LOC_Os10g38890.1 synonymous_variant ; p.Glu94Glu; LOW synonymous_codon Average:30.41; most accessible tissue: Callus, score: 65.274 N N N N
vg1020720683 C -> DEL LOC_Os10g38890.1 N frameshift_variant Average:30.41; most accessible tissue: Callus, score: 65.274 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1020720683 NA 2.36E-15 mr1164 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683 NA 5.54E-08 mr1249 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683 NA 5.13E-29 mr1298 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683 NA 2.16E-20 mr1477 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683 NA 1.10E-46 mr1509 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683 8.45E-06 NA mr1510 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683 2.16E-08 8.83E-63 mr1558 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683 NA 1.51E-20 mr1580 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683 NA 8.35E-10 mr1714 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683 NA 3.60E-26 mr1731 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683 NA 3.35E-12 mr1744 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683 NA 4.36E-29 mr1793 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683 NA 3.54E-17 mr1825 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683 NA 2.78E-11 mr1938 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683 NA 3.18E-21 mr1943 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683 NA 1.04E-16 mr1950 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683 NA 4.89E-19 mr1167_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683 NA 1.19E-47 mr1509_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683 3.47E-06 1.76E-72 mr1558_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683 NA 4.79E-17 mr1578_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683 NA 6.74E-20 mr1581_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683 NA 1.99E-21 mr1698_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683 NA 1.38E-19 mr1746_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683 NA 1.32E-07 mr1819_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020720683 NA 5.77E-15 mr1950_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251